Isolated proteins containing portions of fapalpha and other proteins

ABSTRACT

The invention involves dimeric forms of the protein known as fibroblast activation protein alpha, or “FAPα” and its uses.

RELATED APPLICATION

[0001] This application is a continuation-in-part of Ser. No. 08/230,491, filed Apr. 20, 1994, now pending and incorporated by reference.

FIELD OF THE INVENTION

[0002] This invention relates to certain molecules associated with cancer tissues and reactive tumor stromal cells. More particularly, it relates to fibroblast activation protein alpha (“FAPα” hereafter) molecules. A monomeric form of the molecule has previously been identified immunochemically, but nucleic acid molecules coding for it had not been isolated or cloned nor have dimers been identified. These, inter alia, are features of the invention. The monomeric protein has a molecular weight of from about 88 to about 95 kilodaltons as determined by SDS-PAGE of boiled samples. The dimer has a molecular weight of about 170 kilodaltons as determined by SDS-PAGE of unboiled samples. FAPα is characterized by a number of features and properties which are shared by and characteristic of membrane bound enzymes, suggesting very strongly that it, too, is a membrane bound enzyme. The nucleic acid molecules, which are a key part of the invention, are useful both as probes for cells expressing FAPα, and as starting materials for recombinant production of the protein. The FAPα protein can then be used to produce monoclonal antibodies specific for the protein and are thus useful diagnostic agents themselves. They also have additional uses, including uses related to enzymatic functions, as described herein.

BACKGROUND AND PRIOR ART

[0003] The invasive growth of epithelial cancers is associated with characteristic cellular and molecular changes in the supporting stroma. For example, epithelial cancers induce the formation of tumor blood vessels, the recruitment of reactive tumor stromal fibroblasts, lymphoid and phagocytic infiltrates, the release of peptide mediators and proteolytic enzymes, and the production of an altered extracellular matrix (ECM). See, e.g., Folkman, Adv. Cancer Res. 43: 175-203 (1985); Basset et al., Nature 348: 699-704 (1990); Denekamp et al., Cancer Metastasis Rev. 9: 267-282 (1990); Cullen et al., Cancer Res. 51: 4978-4985 (1991); Dvorak et al., Cancer Cells 3: 77-85 (1991); Liotta et al., Cancer Res. 51: 5054s-5059s (1991); Garin-Chesa et al., J. Histochem. Cytochem. 37: 1767-1776 (1989). A highly consistent molecular trait of the stroma in several common histologic types of epithelial cancers is induction of the fibroblast activation protein (FAPα), a cell surface glycoprotein with an observed M_(r) of 95,000 originally discovered with a monoclonal antibody, mAb F19, raised against proliferating cultured fibroblasts. See Rettig et al., Cancer Res. 46: 6406-6412 (1986); Rettig et al., Proc. Natl. Acad. Sci. USA 85: 3110-3114 (1988); Garin-Chesa et al., Proc. Natl. Acad. USA 87: 7235-7239 (1990); Rettig et al., Cancer Res. 53: 3327-3335 (1993). Each of these four papers is incorporated by reference in its entirety.

[0004] Immunohistochemical studies such as those cited supra have shown that FAPα is transiently expressed in certain normal fetal mesenchymal tissues but that normal adult tissues are generally FAPα⁻. Similarly, malignant epithelial, neural and hematopoietic cells are generally FAPα⁻. However, most of the common types of epithelial cancers, including >90% of breast, lung, skin, pancreas, and colorectal carcinomas, contain abundant FAPα⁺ reactive stromal fibroblasts. Garin-Chesa et al., Proc. Natl. Acad. Sci. USA 87: 7235-7239 (1990). The FAPα⁺ tumor stromal fibroblasts almost invariably accompany tumor blood vessels, forming a distinct cellular compartment interposed between the tumor capillary endothelium and the basal aspect of malignant epithelial cell clusters. While FAPα⁺ stromal fibroblasts are found in both primary and metastatic carcinomas, benign and premalignant as epithelial lesions, such as fibroadenomas of the breast and colorectal adenomas only rarely contain FAPα⁺ stromal cells. In contrast to the stroma-specific localization of FAPα in epithelial neoplasms, FAPα is expressed in the malignant cells of a large proportion of bone and soft tissue sarcomas. (Rettig et al., Proc. Natl. Acad. Sci. USA 85: 3110-3114 (1988)). Finally, FAPα⁺ fibroblasts have been detected in the granulation tissue of healing wounds (Garin-Chesa et al., supra). Based on the restricted distribution pattern of FAPα in normal tissues and its uniform expression in the supporting stroma of many epithelial cancers, clinical trials with ¹³¹I-labeled mAb F19 have been initiated in patients with metastatic colon cancer (Welt et al., Proc. Am. Assoc. Cancer Res. 33: 319 (1992); Welt et al. J. Clin. Oncol. 12: 1561-1571 (1994)) to explore the concept of “tumor stromal targeting” for immunodetection and immunotherapy of epithelial cancers.

[0005] Rettig et al., Int. J. Cancer 58: 385-392 (1994), incorporated by reference, discusses the FAPα molecule and its features. Rettig et al postulate that FAPα is found in high molecular weight complexes in excess of 400 kilodaltons, but do not discuss the possibility of dimeric molecules, nor does the paper elaborate on the specific enzymatic properties of the molecule.

[0006] The induction of FAPα⁺ fibroblasts at times and sites of tissue remodeling during fetal development, tissue repair, and carcinogenesis is consistent with a fundamental role for this molecule in normal fibroblast physiology. Thus, it is of interest and value to isolate and to clone nucleic acid molecules which code for this molecule. This is one aspect of the invention, which is described in detail together with other features of the invention, in the disclosure which follows. Further aspects of the invention include the dimeric FAPα molecules, and the exploitation of the properties of these molecules. These features are also elaborated upon hereafter.

BRIEF DESCRIPTION OF THE FIGURES

[0007]FIG. 1 compares the deduced amino acid sequence for FAPα, and the known sequence of CD26. The alignment has been optimized.

[0008] FIGS. 2A-2H, inclusive, display immunohistochemical detection of FAPα and CD26 in various tissues. In FIGS. 2A and 2B, breast cancer is studied, for FAPα (FIG. 2A), and CD26 (FIG. 2B). In FIGS. 2C and 2D, malignant fibrous histiocytoma is studied, for FAPα (FIG. 2C), and CD26 (FIG. 2D). Dermal scar tissue is examined in FIGS. 2E (FAPα), and 2F (CD26). Renal cell carcinoma is studied in FIG. 2G (FAPα), and 2H (CD26).

[0009]FIG. 3 presents some of the data generated in experiments which showed that FAPα had extracellular matrix (ECM) protein degrading activity. When zymographic detection of gelatin degrading extracts of 293-FAP was carried out, the active substance was found to have a molecular weight of about 170 kD, via SDS-PAGE, using unboiled samples to preserve enzyme activity.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS EXAMPLE 1

[0010] Fibroblast cell line WI-38 had been observed, previously, to react with mAb F19 (Rettig et al., Canc. Res. 46: 6406-6412 (1986); Rettig et al., Proc. Natl. Acad. USA 85: 3110-3114 (1988); Garin-Chesa et al., Proc. Natl. Acad. Sci. USA 87: 7235-7239 (1990); Rettig et al., Canc. Res. 53: 3327-3335 (1993)). It was used in the experiments which follow.

[0011] A cDNA library was prepared from WI-38, using well known techniques and commercially available materials. Specifically, the library was constructed in expression vector pCDNAI, using the Fast Track mRNA isolation kit, and Librarian cDNA phagemid system. Once the library was prepared, the vectors were electroporated into cell line E. coli MC 1061/P3. The pCDNAI expression vector contains an antibiotic resistance gene, so the E. coli were selected via antibiotic resistance. The colonies which were resistant were then used in further experiments. The plasmid DNA from the colonies was obtained via alkaline lysis and purification on CsCl₂, in accordance with Sambrook et al, Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Lab, Cold Spring Harbor, N.Y. 2d Ed. 1989). The technique is well known to the art, but is incorporated by reference herein.

[0012] Once the plasmid DNA was isolated, it was used to transfect COS-1 cells, which were then cultured for forty-eight hours, after which these were tested with antibody coated dishes. The mAbs used included F19, as described by Rettig et al., (1986), supra, which is incorporated by reference in-its entirety. As COS-1 cells are normally FAPα⁻, any positive results indicated the presence of the coding sequence. The immunoselection protocol was that of Aruffo et al., Proc. Natl. Acad. Sci USA 84: 3365-3369 (1987), incorporated by reference herein.

[0013] Plasmid DNA from positive clones was recovered, in accordance with Hirt, J. Mol. Biol. 26: 365-369 (1967), reintroduced into E. coli MC 1061/P3, and reselected in COS-1 cells.

[0014] The protocol presented herein was followed for four rounds. After this, the plasmid DNA of 50 isolated bacterial colonies was purified, using the Qiagen plasmid kit. Of the colonies, 27 clones were found to contain identical 2.8 kb inserts, as determined by EcoRI restriction enzyme mapping. Several of these were found to contain FAPα-specific cDNA as determined by transient expression in COS-1 cells and direct immunofluorescence staining with mAb F19. One of these clones, i.e., “pFAP.38” was selected for further study, as elaborated upon infra.

EXAMPLE 2

[0015] Once pFAP.38 had been identified, it was tested together with a vector coding for known cell surface marker CD26 (“pCD26”), as well as with control vector pCDNA I.

[0016] In these experiments, COS-1 cells were transfected with one of pFAP.38, pCD26, or pCDNAI. After forty-eight hours, the transfectants were tested, using the well known MHA rosetting assay for cell surface antigen expression. In these experiments, mAb F19, which is FAPα specific, was used, together with mAb EF-1, which is CD26 specific. Also used were four other FAPα specific mAbs, i.e., FB23, FB52, FB58 and C48. Also tested were two cancer cell lines, which are known to react with mAb F19 (SW872 liposarcoma) , or EF-1 (SK-OV6 ovarian cancer) . The results are set forth in Table 1, which follows. TABLE 1 Cell surface expression of multiple FAPα epitopes and CD26 in human cells and COS-1 cell transfectants Cell surface antigen expression Target cell F19 FB23 FB52 FB58 C48 EF-1 Human cells SW872 liposarcoma >95% >95% >95% >95% >95% — SK-OV6 ovarian cancer — — — — — >95% COS-1 transfectants COS . pCDNAI control — — — — — — COS . pFAP 38 40% 30% 40% 20% 20% — COS . pCD26 — — — — — 40%

EXAMPLE 3

[0017] Immunoprecipitation studies were then carried out to identify the antigen being targeted by the antibodies.

[0018] Cells were metabolically labelled with Trans ³⁵S-label, (ICN), extracted with lysis buffer (0.01M Tris-HCl/0.15M NaCl/0.01M MgCl₂/0.5% Nonidet P-40/aprotinin (20 ug/ml)/2 mM phenylmethyl-sulf onyl fluoride) , and then immunoprecipitated. The protocols used are all well known, as will be seen by reference to Rettig et al., Canc. Res. 53: 3327-3335 (1993); and Fellinger et al., Canc. Res. 51: 336-340 (1991), the disclosures of which are all incorporated by reference in their entirety. Precipitating mAbs were negative control mouse Ig, mAb F19, or EF-1. Control tests were carried out with mock transfected COS-1 cells. Following immunoprecipitation, the immunoprecipitates were boiled in extraction buffer and separated by NaDOdSO₄/PAGE, under reducing conditions. In some experiments, an additional test was carried out to determine whether or not the immunoprecipitated material was glycosylated. In these experiments, cell extracts were fractionated with Con A-SEPHAROSE prior to immunoprecipitation. Following immunoprecipitation, but prior to fractionation on NaDodSO₄/PAGE, these precipitates were digested with N-Glycanase.

[0019] The results showed that, in COS-1 cells, pFAP.38 directs expression of an 88 kd protein species (as determined via SDS-PAGE), which is slightly smaller than the 95 kd FAPα species produced by SW872, or cultured fibroblasts. Digestion with N-Glycanase produced peptides of comparable size (i.e., 74 kd versus 75 kd), showing that the glycosylation of the FAPA protein in COS-1 cells is different than in the human cell lines.

EXAMPLE 4

[0020] Classic Northern blot analysis was then carried out, using the mRNA from FAPα⁺ fibroblast cell lines WI-38 and GM 05389, and FAPα⁻ ovarian cancer cell line SK-OV6. Using the procedures of Sambrook et al., supra, five micrograms of mRNA from each cell line were tested. The probes used were ³²P labelled, and were prepared from a 2.3 kb ECO I fragment of pFAP.38, a 2.4 kb Hind III fragment of CD26, and a 1.8 kb BamHI fragment of γ-actin cDNA. These fragments had been purified from 1% agarose gels.

[0021] The extracts of FAPα⁺ fibroblast strains showed a 2.8 kb FAP mRNA species, but extracts of SK-OV6 do not. A γ-actin mRNA species (1.8 kb), was observed in all species.

EXAMPLE 5

[0022] The cDNA identified as coding for FAPα was subjected to more detailed analysis, starting with sequencing. The classic Sanger methodology, as set forth in Proc. Natl. Acad. Sci. USA 74: 5463-5467 (1977), was used to sequence both strands of the cDNA. Once this was secured, an amino acid sequence was deduced therefrom. This information is presented in SEQ ID NO: 1. The sequence was then compared to the known amino acid sequence of CD26 (Morimoto et al., J. Immunol. 143: 3430-3437 (1989)). FIG. 1 presents the comparison, using optimized sequence alignment. Any gaps in the comparison are indicated by asterisks, while identical amino acids are shown by dashes in the CD26 sequence. A hydrophobic, putative transmembrane sequence is double underlined, while potential N-glycosylation sites are single underlined.

[0023] The sequence analysis shows a 2812 base pair insert, wherein 2277 base pairs constitute the open reading frame. This ORF extends from-start codon ATG at nucleotide 209, to stop codon TAA at 2486.

[0024] The deduced polypeptide is 760 amino acids long, and has a molecular weight of 87,832. In contrast, N-Glycanase digested, immunopurified FAPα was reported to have an estimated M_(r) of 75,000 on NaDodSO₄/PAGE (Rettig et al., Canc. Res. 53: 3327-3335 (1993)).

[0025] A GenBank data base search was carried out. The most closely related genes found were those encoding dipeptidyl peptidase IV homologues (DPPIV; EC 3.4.14.5), with human DPPIV (also known as T-cell activation antigen CD26), showing 61% nucleotide sequence identity, and 48% amino acid sequence identity.

[0026] The second set of related genes are human, rat, and bovine homologues of DPPX, a gene of unknown function widely expressed in brain and other normal tissues. The predicted human DPPX gene product shows about 30% amino acid sequence identity with FAPα and CD26. The FAPα molecule exhibits structural features typical of type II integral membrane proteins, including a large COOH-terminal extracellular domain, a hydrophobic transmembrane segment, and a short cytoplasmic tail. The putative extracellular domain contains five potential N-glycosylation sites, eleven cysteine residues (eight of which are conserved between FAPα and CD26), and three segments corresponding to highly conserved catalytic domains characteristic of serine proteases, such as DPPIV. These conserved sequences are presented in Table 2, which follows. Comparisons to DPPIV and DPPX were made via Morimoto et al., supra; Wada et al., Proc. Natl. Acad. Sci. USA 89: 197-201 (1992); Yokotani et al., Human Mol. Genet. 2: 1037-1039 (1993). TABLE 2 Putative catalytic domains of FAPα, DPPIV and DPPX. 624 702 734 Human FAPα . . . . WGWSYGG . . . . . . . . GTADDNV . . . . . . . . DQNHGLS . . . . Human DPPIV . . . . WGWSYGG . . . . . . . . GTADDNV . . . . . . . . DEDHGIA . . . . Mouse DPPIV . . . . WGWSYGG . . . . . . . . GTADDNV . . . . . . . . DEDHGIA . . . . Rat DPPIV . . . . WGWSYGG . . . . . . . . GTADDNV . . . . . . . . DEDHGIA . . . . Yeast DPPIV . . . . FGWSYGG . . . . . . . . GTGDDNV . . . . . . . . DSDHSIR . . . . Human DPPX . . . . FGKDYGG . . . . . . . . PTADEKI . . . . . . . . DESHYFT . . . . Rat DPPX . . . . FGKDYGG . . . . . . . . ATADEKI . . . . . . . . DESHYFH . . . . Bovine DPPX . . . . FGKDYGG . . . . . . . . ATADEKI . . . . . . . . DESHYFS . . . .

EXAMPLE 6

[0027] An additional set of experiments were carried out to determine whether FAPα related sequences are present in non-human species. To do so, human, mouse, and Chinese hamster genomic DNA was digested using restriction enzymes, and tested, via Southern blotting, using the 2.3 kb fragment, labelled with ³²P, describes supra. Hybridization was carried out using stringent washing conditions (0.1×SSC, 0.1.NaDodSO₄, 68° C.). Cross-hybridization was readily observed with both the mouse and hamster DNA, suggesting the existence of highly conserved FAPα homologues. In control experiments using the CD26 cDNA fragment described supra, no evidence of cross hybridization was observed.

EXAMPLE 7

[0028] The CD26 molecule shares a number of biochemical and serological properties with FAPβ, which is a previously described, FAPα associated molecule having a molecular weight of 105 kd, and is found on cultured fibroblasts and melanocytes (Rettig et al., Canc. Res. 53: 3327-3335 (1993)). Cotransfection experiments were carried out to determine whether FAPβ is a CD26 gene product. To test this, the same protocols were used which were used for transfection with pFAP.38 or pCD26, as described supra, but using the two vectors. The results presented supra showed that cotransfection efficiency was about 40% for each vector, so about 10-20% of cell should be cotransfected.

[0029] Following cotransfection, the COS-1 cells were Trans ³⁵S-labeled, as described supra, then lysed, also as described supra.

[0030] The resulting cell extracts were separated on Con A SEPHAROSE, and the antigen (FAPα and/or CD26) were recovered in the Con A-bound fraction. The bound fraction was eluted with 0.25M α-D-mannopyranoside. Immunoprecipitation was then carried out, as described supra, and the precipitates were separated on NaDodSO₄/PAGE, also as discussed supra.

[0031] Those cells transfected only with pFAP.38 produced FAPα, but not FAPβ (determined from mAb F19 immunoprecipitates). They also produce no CD26 antigen (tested with EF-1). Those cells transfected with pCD26 alone produce CD26 but no FAPα. Cotransfectants produce CD26 and FAPα/FAPβ heteromers, as determined in the mAb F19 precipitates. This result provides direct evidence that FAPβ is a CD26 gene product.

EXAMPLE 8

[0032] It has been observed previously that some cultured human cell types coexpress FAPα and CD26, and show FAPα/CD26 heteromer formation. In vivo distribution patterns of FAPα and CD26, however, as determined in previous immunohistochemical studies, appeared to be-non-overlapping. (See Rettig et al., Proc. Natl. Acad. Sci. USA 85: 3110-3114 (1988); Garin-Chesa et al., Proc. Natl. Acad. Sci. USA 87: 7235-7329 (1990); Rettig et al., Canc. Res. 53: 3327-3335 (1993); Stein et al., in Knapp et al., eds. Leukocyte typing IV-white cell differentiation antigens, pp. 412-415 (Oxford University Press, N.Y. 1989), pp. 412-415; Möbious et al., J. Exp. Immunol. 74: 431-437 (1988)). In view of the potential significance of FAPα/CD26 coassociation, tissue distribution was reexamined, via side by side immunohistochemical staining of normal tissues and lesional tissues known to contain FAPAα⁺ fibroblasts or FAPα⁺ malignant cells.

[0033] To test the samples, they were embedded in OCT compound, frozen in isopentane precooled in liquid nitrogen, and stored at −70° C. until used. Five micrometer thick sections were cut, mounted on poly-L-lysine coated slides, air dried, and fixed in cold acetone (4° C., for 10 minutes). The sections were then tested with mAbs (10-20 ug/ml), using the well known avidin-biotin immmuno-peroxidase method, as described by, e.g., Garin-Chesa et al., J. Histochem. Cytochem. 37: 1767-1776 (1989); Garin-Chesa et al., Proc. Natl. Acad. Sci. USA 87: 7235-7239 (1990); Rettig et al., Canc. Res. 53: 3327-3335 (1993); Garin-Chesa et al., Am. J. Pathol. 142: 557-567.

[0034] The results are shown in FIG. 2. Breast, colorectal, pancreas and lung carcinomas showed strong expression of FAPα and no CD26 was found (see FIGS. 2A and 2B). Five FAPα⁺ sarcomas, including malignant fibrous histiocytoma (FIGS. 2C and 2D), were tested, and there was no expression of CD26. Examination of reactive fibroblasts of healing dermal wounds (FIGS. 2E, 2F), showed abundant expression of both FAPα and CD26. The three renal carcinomas tested (FIGS. 2G, 2H), showed expression of CD26 in malignant epithelium. FAPα was absent from malignant epithelial cells, and showed low expression in the stroma of these carcinomas.

EXAMPLE 9

[0035] A mammalian cell line, transfected with a FAPα encoding CDNA, was prepared.

[0036] Human embryonic kidney cell line 293 is well known and widely available from, e.g., the American Type Culture Collection.

[0037] Samples of 293 were maintained, in an incubator, at 37° C., in an atmosphere of 95% air, and 5% CO₂. The cells were cultured in a 50:50 mixture of Dulbecco's modified minimal essential medium and Ham's F12 medium, augmented with 10% fetal bovine serum, penicillin and streptomycin. Following the procedures described by Ustar et al., Eur. Mol. Biol. J. 1991, and/or Park et al., J. Biol. Chem. 169: 25646-25654 (1994), both of which are incorporated by reference, cDNA for FAPα (i.e., SEQ ID NO: 1), was transfected into the 293 cells. Details of the cDNA vector are provided, supra (pFAP.38). Transfectants were selected for resistance to antibiotics (200 ug/ml Geneticin), and were then maintained in selection medium, containing Geneticin.

[0038] Individual colonies of resistant cells were picked, grown to confluence in 6 well tissue culture plates, and were tested for FAPα expression in an immunofluorescence assay (IFA), using FAPα specific monoclonal antibody F19 as described supra.

[0039] Those colonies which expressed FAPα were expanded, and monitored by indirect IFA and cytofluorometric analysis, also as set forth, supra.

[0040] The IFAs were positive for the transfectants, referred to hereafter as cell line 293-FAP, but were negative for parental line 293.

EXAMPLE 10

[0041] In order to confirm that recombinant FAPα was, in fact, being produced, a series of immunoprecipitation experiments were carried out. These followed the methods of Park, et al., supra, and Rettig et al., Canc. Res. 53: 3327-3335 (1993), both of which are incorporated by reference. Essentially, ³⁵[S] methionine labelled cell extracts were combined with monoclonal antibody F19, in the manner described supra. Precipitates were then boiled in extraction buffer and run on SDS-PAGE gels, using, as a negative control, mouse IgGl. Both cell line 293-FAP, and non transfected line 293 were tested. The results indicated clearly, that recombinant FAPα was produced by the transfected cell line 293-FAP. This was determined by immunoprecipitation analyses, using FAPα specific monoclonal antibody F19.

EXAMPLE 11

[0042] The ability to produce recombinant FAPα permitted further study of the molecule's properties. Specifically, given the structural features outlined in the prior examples, experiments were designed to determine if FAPα possesses enzymatic activities. The experiments were designed to test whether or not FAPα had extracellular matrix (ECM) protein degrading activity.

[0043] Extracts of 293-FAP cells were prepared, using an extraction buffer (0.15M NaCl, 0.05M Tris-HCl, pH 7.4, 10 mM MgCl₂, 1 percent Triton X-114), were cleared by centrifugation (4,000 xg, 10 minutes at 40° C.), and phase partitioned at 37° C. for 10-20 minutes. This was followed by further centrifugation (4000 xg, 20 minutes at 20-25° C.) Detergent phases were diluted with buffer (0.15M NaCl, 0.05M Tris-HCl pH 7.4, 5 mM CaCl₂, 5 mM MgCl₂, 0.75% Empigen BB), and separated on concanavalin A-Sepharose following Rettig et al., supra. Any concanavalin A bound fractions were eluted with 0.25M methyl-α-D-mannopyranoside in elution buffer 0.15M NaCl,0.05M Tris-HCl, pH 7.4, 5 mM CaCl₂, 5 mM MgCl₂, 0.1% Triton X-100), mixed with zymography sample buffer (0.25M Tris-HCl, pH 6.8, 8% SDS, 40% glycerol, 0.01% bromophenol blue), at a 3:1 ratio, and used for further analysis.

[0044] Aliquots of sample were loaded onto polyacrylamide gels containing 0.1% of either of gelatin or casein. Electrophoresis was then carried out in a Biorad Mini-Protein II system,.at 20 mA constant current for 1.5-2 hours, until the bromophenol blue due fronts of samples had reached the lower end of the gel. The gel was removed and incubated for one hour at 20-25° C. in a 2.5% aqueous solution of Triton X-100 on a rotary shaker. The Triton X-100 solution was decanted, and replaced with enzyme buffer (0.05M Tris-HCl, pH 7.5, 0.2M NaCl, 5 mM CaCl₂, 5 mM MgCl₂, 0.02% Brij 35). The gel was then incubated at 37° C. or 41° C., followed by staining or destaining at room temperature. Gels were stained with 0.5% of Coomassie Brilliant Blue G-250 in an aqueous solution of 30% methanol and 10% acetic acid for 15, 30, and 60 minutes, respectively. Subsequently, gels were incubated for 15 minutes in an aqueous solution of 30% CH₃OH and 5% glycerol, followed by drying between sheets of cellophane.

[0045] Gelatinase activity was evaluated in accordance with Kleiner et al., Anal. Biochem. 218: 325-329 (1994), incorporated by reference in its entirety. This is a routine assay used to determine whether or not a protease capable of digesting gelatin is present. Labelled molecular weight standard were run on the same gels, under reducing conditions, for molecular weight determinations.

[0046] Proteolytic activity for defined amino acid sequence motifs were tested, using a well known membrane overlay assay. See Smith et al, Histochem. J. 24(9): 637-647 (1992), incorporated by reference. Substrates were Ala-Pro-7-amino-4-trifluoromethyl coumarin, Gly-Pro-7-amino-4-trifluoromethyl coumarin, and Lys-Pro-7-amino-4-trifluromethyl coumarin.

[0047] The results of these experiments are depicted, in part, in FIG. 3. This figure shows zymographic detection of gelatin degrading activity, in the cell extracts. See Kleiner et al., supra. A protein species of approximately 170 kilodaltons, as determined by SDS-PAGE, was observed to have gelatin degrading activity. This species, which was found in the 293-FAP cell line, but not in untransfected 293 cells, is thus identified as FAPα. The molecular weight is consistent with a dimer, i.e., a dimeric FAPα molecule.

[0048] The proteolytic activity described herein where gelatin is the substrate, was not observed when casein was the substrate.

EXAMPLE 12

[0049] Further studies were then undertaken in order to characterize the 170 kD FAPα dimer further. Specifically, the experiments described in example 11 were repeated, except that 5% of 2-mercaptoethanol or 5 um iodoacetamide was added to the extracts prior to SDS-PAGE, or ethylenediamine N,N,N′,N′-tetraacetic acid (10 mM) was added to the incubation buffer used for gelatin zymography. None of these treatments abolished the enzymatic activity. In contrast, heating at 100° C. for five minutes prior to SDS-polyacrylamide gel electrophoresis abolished the gelatin-degrading activity.

[0050] Further work, using a membrane overlay assay, described by, e.g., Smith et al., Histochem J. 24(9): 643-647 (1992), incorporated by reference, revealed that the FAPα dimers were able to cleave all of the Ala-Pro, Gly-Pro, and Lys-Pro dipeptides tested.

[0051] In further experiments, a fusion protein was produced which comprised the extracellular domains of both FAPα and murine CD8 proteins. This chimeric protein was produced in a baculovirus system in insect cells. The chimeric protein exhibited the same enzymatic activity as FAPα, using the model discussed supra.

[0052] The foregoing examples describe an isolated nucleic acid molecule which codes for fibroblast activating protein alpha (“FAPα”), as well as dimeric forms of the molecule, and uses thereof. The expression product of the sequence in COS-1 is a protein which, on SDS-PAGE of boiled samples, shows a molecular weight of about 88 kd. Deduced amino acid sequence, as provided in SEQ ID NO: 1, for one form of the molecule, yields a molecular weight of about 88 kd.

[0053] It should be noted that there is an apparent discrepancy in molecular weight in that the COS-1 isolate is glycosylated, while molecular weight from deduced amino acid sequences does not account for glycosylation. Membrane proteins are known to exhibit aberrant migration in gel systems, however, which may explain the difference observed here.

[0054] Also a part of the invention are chimeric and fusion proteins, which comprise a portion of FAPα which contain the molecule's catalytic domain, and additional, non FAPα components. The FAPα catalytic domain per se is also a part of the invention.

[0055] It is to be understood that, as described, FAPα may be glycosylated, with the type and amount of glycosylation varying, depending upon the type of cell expressing the molecule. The experiment described herein shows this. This is also true for the dimeric form of the molecule, first described herein, having a molecular weight of about 170 kilodaltons as determined by SDS-PAGE of unboiled samples.

[0056] The invention also comprehends the production of expression vectors useful in producing the FAPα molecule. In their broadest aspect, these vectors comprise the entire FAPα coding sequence or portions thereof, operably linked to a promoter. Additional elements may be a part of the expression vector, such as protein domains fused to the FAPα protein or protein portions (“fusion protein”) genes which confer antibiotic resistance, amplifiable genes, and so forth.

[0057] The coding sequences and vectors may also be used to prepare cell lines, wherein the coding sequence or expression vector is used to transfect or to transform a recipient host. The type of cell used may be prokaryotic, such as E. coli, or eukaryotes, such as yeast, CHO, COS, or other cell types.

[0058] The identification of nucleic acid molecules such as that set forth in SEQ ID NO: 1 also enables the artisan to identify and to isolate those nucleic acid molecules which hybridize to it under stringent conditions. “Stringent condition” as used herein, refers to those parameters set forth supra, whereby both murine and hamster sequences were also identified. It will be recognized by the skilled artisan that these conditions afford a degree of stringency which can be achieved using parameters which vary from those recited. Such variance is apprehended by the expression “stringent conditions”.

[0059] The ability of nucleic acid molecules to hybridize to complementary molecules also enables the artisan to identify cells which express FAPα, via the use of a nucleic acid hybridization assay. One may use the sequences described in the invention to hybridize to complementary sequences, and thus identify them. In this way, one can target mRNA, e.g., which is present in any cell expressing the FAPα molecule.

[0060] It is of course understood that the nucleic acid molecules of the invention are also useful in the production of recombinant FAPα, in both monomeric and dimeric form. The examples clearly show that host cells are capable of assembling the dimeric forms. The recombinant protein may be used, e.g., as a source of an immunogen for generation of antibodies akin to known mAb F19, and with the same uses. Similarly, the recombinant protein, and/or cells which express the molecule on their surface, may be used in assays to determine antagonists, agonists, or other molecules which interact with the FAPα molecule. Such molecules may be, but are not necessarily limited to, substrates, inhibiting molecules, antibodies, and so forth. This last feature of the invention should be considered in light of the observed structural resemblances to membrane bound enzymes. This type of molecule is associated with certain properties which need not be described in detail here. It will suffice to say that inhibition or potentiation of these properties as associated with FAPα is a feature of this invention. For example, one may identify substrates or the substrate for FAPα molecules, via the use of recombinant cells or recombinant FAPα per se. The substrates can be modified to improve their effect, to lessen their effect, or simply to label them with detectable signals so that they can be used, e.g., to identify cells which express FAPα. Study of the interaction of substrate and FAPα, as well as that between FAPα and any molecule whatsoever, can be used to develop and/or to identify agonists and antagonists of the FAPα molecule.

[0061] Also a feature of the invention are isolated, dimeric FAPα molecules which have a molecular weight of about 170 kilodaltons as determined by SDS-PAGE, their use as an enzymatic cleaving agent, and other uses as are described herein. Enzymatically active forms of FAPα may also be produced as recombinant fusion proteins, comprising the catalytic domain of FAPα and other protein domains with suitable biochemical properties, including secretory signals protease cleavage sites, tags for purification, and other elements known to the artisan. The fact that FAPα has particular properties, as described herein, permits the identification of the molecule on cells expressing them. In turn, because the FAPα molecule is associated with tumors and tumor stromal cells, targeting of FAPα with therapeutic agents serves as a way to treat cancerous or precancerous condition, by administering sufficient therapeutic agent to alleviate cancer load.

[0062] The experiments showing the proteolytic properties of FAPα lead to yet a further aspect of the invention. It is well known that proteases which degrade extracellular matrix, or “ECM” proteins have an important role on certain aspects of tumor growth, including their effect on tumor cell invasion, tumor blood vessel formation (i.e., neoangiogenesis), and tumor metastasis. Collagens are of special interest vis-a-vis the substrates of proteases, as the collagens are an important part of the ECM. The fact that FAPα digests ECM suggests a therapeutic role for inhibitors of the molecule. “Inhibitors”, as used herein, refers to molecules which interfere with FAPα enzyme function. Specifically excluded from such inhibitors is the monoclonal antibody F19. This mAb is known to bind to but not inhibit the enzyme function of FAPα, and hence it is not an inhibitor. The art is quite well versed with respect to monoclonal antibodies which both bind to and inhibit enzymes. Further examples of such inhibitors would include, e.g., substrate derivatives, such as modified collagen molecules, which interfere with the active site or sites of the FAPα molecule. Other suitable inhibitors will be apparent to the skilled artisan, and need not be listed here. In addition, the recombinant FAPα proteins and FAPα-transfected cell lines described supra can be employed in an enzymatic screening assay, using the substrate described supra or other suitable substrates, to identify inhibitors from any compound library.

[0063] Other aspects of the invention will be clear to the skilled artisan, and need not be set forth here.

[0064] The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, it being recognized that various modifications are possible within the scope of the invention.

1 10 2815 Base pairs nucleic acid double linear 1 AAGAACGCCC CCAAAATCTG TTTCTAATTT TACAGAAATC TTTTGAAACT TGGCACGGTA 60 TTCAAAAGTC CGTGGAAAGA AAAAAACCTT GTCCTGGCTT CAGCTTCCAA CTACAAAGAC 120 AGACTTGGTC CTTTTCAACG GTTTTCACAG ATCCAGTGAC CCACGCTCTG AAGACAGAAT 180 TAGCTAACTT TCAAAAACAT CTGGAAAAAT GAAGACTTGG GTAAAAATCG TATTTGGAGT 240 TGCCACCTCT GCTGTGCTTG CCTTATTGGT GATGTGCATT GTCTTACGCC CTTCAAGAGT 300 TCATAACTCT GAAGAAAATA CAATGAGAGC ACTCACACTG AAGGATATTT TAAATGGAAC 360 ATTTTCTTAT AAAACATTTT TTCCAAACTG GATTTCAGGA CAAGAATATC TTCATCAATC 420 TGCAGATAAC AATATAGTAC TTTATAATAT TGAAACAGGA CAATCATATA CCATTTTGAG 480 TAATAGAACC ATGAAAAGTG TGAATGCTTC AAATTACGGC TTATCACCTG ATCGGCAATT 540 TGTATATCTA GAAAGTGATT ATTCAAAGCT TTGGAGATAC TCTTACACAG CAACATATTA 600 CATCTATGAC CTTAGCAATG GAGAATTTGT AAGAGGAAAT GAGCTTCCTC GTCCAATTCA 660 GTATTTATGC TGGTCGCCTG TTGGGAGTAA ATTAGCATAT GTCTATCAAA ACAATATCTA 720 TTTGAAACAA AGACCAGGAG ATCCACCTTT TCAAATAACA TTTAATGGAA GAGAAAATAA 780 AATATTTAAT GGAATCCCAG ACTGGGTTTA TGAAGAGGAA ATGCTTCCTA CAAAATATGC 840 TCTCTGGTGG TCTCCTAATG GAAAATTTTT GGCATATGCG GAATTTAATG ATAAGGATAT 900 ACCAGTTATT GCCTATTCCT ATTATGGCGA TGAACAATAT CCTAGAACAA TAAATATTCC 960 ATACCCAAAG GCTGGAGCTA AGAATCCCGT TGTTCGGATA TTTATTATCG ATACCACTTA 1020 CCCTGCGTAT GTAGGTCCCC AGGAAGTGCC TGTTCCAGCA ATGATAGCCT CAAGTGATTA 1080 TTATTTCAGT TGGCTCACGT GGGTTACTGA TGAACGAGTA TGTTTGCAGT GGCTAAAAAG 1140 AGTCCAGAAT GTTTCGGTCC TGTCTATATG TGACTTCAGG GAAGACTGGC AGACATGGGA 1200 TTGTCCAAAG ACCCAGGAGC ATATAGAAGA AAGCAGAACT GGATGGGCTG GTGGATTCTT 1260 TGTTTCAAGA CCAGTTTTCA GCTATGATGC CATTTCGTAC TACAAAATAT TTAGTGACAA 1320 GGATGGCTAC AAACATATTC ACTATATCAA AGACACTGTG GAAAATGCTA TTCAAATTAC 1380 AAGTGGCAAG TGGGAGGCCA TAAATATATT CAGAGTAACA CAGGATTCAC TGTTTTATTC 1440 TAGCAATGAA TTTGAAGAAT ACCCTGGAAG AAGAAACATC TACAGAATTA GCATTGGAAG 1500 CTATCCTCCA AGCAAGAAGT GTGTTACTTG CCATCTAAGG AAAGAAAGGT GCCAATATTA 1560 CACAGCAAGT TTCAGCGACT ACGCCAAGTA CTATGCACTT GTCTGCTACG GCCCAGGCAT 1620 CCCCATTTCC ACCCTTCATG ATGGACGCAC TGATCAAGAA ATTAAAATCC TGGAAGAAAA 1680 CAAGGAATTG GAAAATGCTT TGAAAAATAT CCAGCTGCCT AAAGAGGAAA TTAAGAAACT 1740 TGAAGTAGAT GAAATTACTT TATGGTACAA GATGATTCTT CCTCCTCAAT TTGACAGATC 1800 AAAGAAGTAT CCCTTGCTAA TTCAAGTGTA TGGTGGTCCC TGCAGTCAGA GTGTAAGGTC 1860 TGTATTTGCT GTTAATTGGA TATCTTATCT TGCAAGTAAG GAAGGGATGG TCATTGCCTT 1920 GGTGGATGGT CGAGGAACAG CTTTCCAAGG TGACAAACTC CTCTATGCAG TGTATCGAAA 1980 GCTGGGTGTT TATGAAGTTG AAGACCAGAT TACAGCTGTC AGAAAATTCA TAGAAATGGG 2040 TTTCATTGAT GAAAAAAGAA TAGCCATATG GGGCTGGTCC TATGGAGGAT ACGTTTCATC 2100 ACTGGCCCTT GCATCTGGAA CTGGTCTTTT CAAATGTGGT ATAGCAGTGG CTCCAGTCTC 2160 CAGCTGGGAA TATTACGCGT CTGTCTACAC AGAGAGATTC ATGGGTCTCC CAACAAAGGA 2220 TGATAATCTT GAGCACTATA AGAATTCAAC TGTGATGGCA AGAGCAGAAT ATTTCAGAAA 2280 TGTAGACTAT CTTCTCATCC ACGGAACAGC AGATGATAAT GTGCACTTTC AAAACTCAGC 2340 ACAGATTGCT AAAGCTCTGG TTAATGCACA AGTGGATTTC CAGGCAATGT GGTACTCTGA 2400 CCAGAACCAC GGCTTATCCG GCCTGTCCAC GAACCACTTA TACACCCACA TGACCCACTT 2460 CCTAAAGCAG TGTTTCTCTT TGTCAGACTA AAAACGATGC AGATGCAAGC CTGTATCAGA 2520 ATCTGAAAAC CTTATATAAA CCCCTCAGAC AGTTTGCTTA TTTTATTTTT TATGTTGTAA 2580 AATGCTAGTA TAAACAAACA AATTAATGTT GTTCTAAAGG CTGTTAAAAA AAAGATGAGG 2640 ACTCAGAAGT TCAAGCTAAA TATTGTTTAC ATTTTCTGGT ACTCTGTGAA AGAAGAGAAA 2700 AGGGAGTCAT GCATTTTGCT TTGGACACAG TGTTTTATCA CCTGTTCATT TGAAGAAAAA 2760 TAATAAAGTC AGAAGTTCAA AAAAAAAAAA AAAAAAAAAA AAAGCGGCCG CTCGA 2815 760 amino acids amino acid linear 2 Met Lys Thr Trp Val Lys Ile Val Phe Gly Val Ala Thr Ser Ala Val 5 10 15 Leu Ala Leu Leu Val Met Cys Ile Val Leu Arg Pro Ser Arg Val His 20 25 30 Asn Ser Glu Glu Asn Thr Met Arg Ala Leu Thr Leu Lys Asp Ile Leu 35 40 45 Asn Gly Thr Phe Ser Tyr Lys Thr Phe Phe Pro Asn Trp Ile Ser Gly 50 55 60 Gln Glu Tyr Leu His Gln Ser Ala Asp Asn Asn Ile Val Leu Tyr Asn 65 70 75 80 Ile Glu Thr Gly Gln Ser Tyr Thr Ile Leu Ser Asn Arg Thr Met Lys 85 90 95 Ser Val Asn Ala Ser Asn Tyr Gly Leu Ser Pro Asp Arg Gln Phe Val 100 105 110 Tyr Leu Glu Ser Asp Tyr Ser Lys Leu Trp Arg Tyr Ser Tyr Thr Ala 115 120 125 Thr Tyr Tyr Ile Tyr Asp Leu Ser Asn Gly Glu Phe Val Arg Gly Asn 130 135 140 Glu Leu Pro Arg Pro Ile Gln Tyr Leu Cys Trp Ser Pro Val Gly Ser 145 150 155 160 Lys Leu Ala Tyr Val Tyr Gln Asn Asn Ile Tyr Leu Lys Gln Arg Pro 165 170 175 Gly Asp Pro Pro Phe Gln Ile Thr Phe Asn Gly Arg Glu Asn Lys Ile 180 185 190 Phe Asn Gly Ile Pro Asp Trp Val Tyr Glu Glu Glu Met Leu Pro Thr 195 200 205 Lys Tyr Ala Leu Trp Trp Ser Pro Asn Gly Lys Phe Leu Ala Tyr Ala 210 215 220 Glu Phe Asn Asp Lys Asp Ile Pro Val Ile Ala Tyr Ser Tyr Tyr Gly 225 230 235 240 Asp Glu Gln Tyr Pro Arg Thr Ile Asn Ile Pro Tyr Pro Lys Ala Gly 245 250 255 Ala Lys Asn Pro Val Val Arg Ile Phe Ile Ile Asp Thr Thr Tyr Pro 260 265 270 Ala Tyr Val Gly Pro Gln Glu Val Pro Val Pro Ala Met Ile Ala Ser 275 280 285 Ser Asp Tyr Tyr Phe Ser Trp Leu Thr Trp Val Thr Asp Glu Arg Val 290 295 300 Cys Leu Gln Trp Leu Lys Arg Val Gln Asn Val Ser Val Leu Ser Ile 305 310 315 320 Cys Asp Phe Arg Glu Asp Trp Gln Thr Trp Asp Cys Pro Lys Thr Gln 325 330 335 Glu His Ile Glu Glu Ser Arg Thr Gly Trp Ala Gly Gly Phe Phe Val 340 345 350 Ser Arg Pro Val Phe Ser Tyr Asp Ala Ile Ser Tyr Tyr Lys Ile Phe 355 360 365 Ser Asp Lys Asp Gly Tyr Lys His Ile His Tyr Ile Lys Asp Thr Val 370 375 380 Glu Asn Ala Ile Gln Ile Thr Ser Gly Lys Trp Glu Ala Ile Asn Ile 385 390 395 400 Phe Arg Val Thr Gln Asp Ser Leu Phe Tyr Ser Ser Asn Glu Phe Glu 405 410 415 Glu Tyr Pro Gly Arg Arg Asn Ile Tyr Arg Ile Ser Ile Gly Ser Tyr 420 425 430 Pro Pro Ser Lys Lys Cys Val Thr Cys His Leu Arg Lys Glu Arg Cys 435 440 445 Gln Tyr Tyr Thr Ala Ser Phe Ser Asp Tyr Ala Lys Tyr Tyr Ala Leu 450 455 460 Val Cys Tyr Gly Pro Gly Ile Pro Ile Ser Thr Leu His Asp Gly Arg 465 470 475 480 Thr Asp Gln Glu Ile Lys Ile Leu Glu Glu Asn Lys Glu Leu Glu Asn 485 490 495 Ala Leu Lys Asn Ile Gln Leu Pro Lys Glu Glu Ile Lys Lys Leu Glu 500 505 510 Val Asp Glu Ile Thr Leu Trp Tyr Lys Met Ile Leu Pro Pro Gln Phe 515 520 525 Asp Arg Ser Lys Lys Tyr Pro Leu Leu Ile Gln Val Tyr Gly Gly Pro 530 535 540 Cys Ser Gln Ser Val Arg Ser Val Phe Ala Val Asn Trp Ile Ser Tyr 545 550 555 560 Leu Ala Ser Lys Glu Gly Met Val Ile Ala Leu Val Asp Gly Arg Gly 565 570 575 Thr Ala Phe Gln Gly Asp Lys Leu Leu Tyr Ala Val Tyr Arg Lys Leu 580 585 590 Gly Val Tyr Glu Val Glu Asp Gln Ile Thr Ala Val Arg Lys Phe Ile 595 600 605 Glu Met Gly Phe Ile Asp Glu Lys Arg Ile Ala Ile Trp Gly Trp Ser 610 615 620 Tyr Gly Gly Tyr Val Ser Ser Leu Ala Leu Ala Ser Gly Thr Gly Leu 625 630 635 640 Phe Lys Cys Gly Ile Ala Val Ala Pro Val Ser Ser Trp Glu Tyr Tyr 645 650 655 Ala Ser Val Tyr Thr Glu Arg Phe Met Gly Leu Pro Thr Lys Asp Asp 660 665 670 Asn Leu Glu His Tyr Lys Asn Ser Thr Val Met Ala Arg Ala Glu Tyr 675 680 685 Phe Arg Asn Val Asp Tyr Leu Leu Ile His Gly Thr Ala Asp Asp Asn 690 695 700 Val His Phe Gln Asn Ser Ala Gln Ile Ala Lys Ala Leu Val Asn Ala 705 710 715 720 Gln Val Asp Phe Gln Ala Met Trp Tyr Ser Asp Gln Asn His Gly Leu 725 730 735 Ser Gly Leu Ser Thr Asn His Leu Tyr Thr His Met Thr His Phe Leu 740 745 750 Lys Gln Cys Phe Ser Leu Ser Asp 755 760 766 amino acids amino acid linear 3 Met Lys Thr Pro Trp Lys Val Leu Leu Gly Leu Leu Gly Ala Ala Ala 5 10 15 Leu Val Thr Ile Ile Thr Val Pro Val Val Leu Leu Asn Lys Gly Thr 20 25 30 Asp Asp Ala Thr Ala Asp Ser Arg Lys Thr Tyr Thr Leu Thr Asp Tyr 35 40 45 Leu Lys Asn Thr Tyr Arg Leu Lys Leu Tyr Ser Leu Arg Trp Ile Ser 50 55 60 Asp His Glu Tyr Leu Tyr Lys Gln Glu Asn Asn Ile Leu Val Phe Asn 65 70 75 80 Ala Glu Tyr Gly Asn Ser Ser Val Phe Leu Glu Asn Ser Thr Phe Asp 85 90 95 Glu Phe Gly His Ser Ile Asn Asp Tyr Ser Ile Ser Pro Asp Gly Gln 100 105 110 Phe Ile Leu Leu Glu Tyr Asn Tyr Val Lys Gln Trp Arg His Ser Tyr 115 120 125 Thr Ala Ser Tyr Asp Ile Tyr Asp Leu Asn Lys Arg Gln Leu Ile Thr 130 135 140 Glu Glu Arg Ile Pro Asn Asn Thr Gln Trp Val Thr Trp Ser Pro Val 145 150 155 165 Gly His Lys Leu Ala Tyr Val Trp Asn Asn Asp Ile Tyr Val Lys Ile 170 175 180 Glu Pro Asn Leu Pro Ser Tyr Arg Ile Thr Trp Thr Gly Lys Glu Asp 185 190 195 Ile Ile Tyr Asn Gly Ile Thr Asp Trp Val Tyr Glu Glu Glu Val Phe 200 205 210 Ser Ala Tyr Ser Ala Leu Trp Trp Ser Pro Asn Gly Thr Phe Leu Ala 215 220 225 Tyr Ala Gln Phe Asn Asp Thr Glu Val Pro Leu Ile Glu Tyr Ser Phe 230 235 240 245 Tyr Ser Asp Glu Ser Leu Gln Tyr Pro Lys Thr Val Arg Val Pro Tyr 250 255 260 Pro Lys Ala Gly Ala Val Asn Pro Thr Val Lys Phe Phe Val Val Asn 265 270 275 Thr Asp Ser Leu Ser Ser Val Thr Asn Ala Thr Ser Ile Gln Ile Thr 280 285 290 Ala Pro Ala Ser Met Leu Ile Gly Asp His Tyr Leu Cys Asp Val Thr 295 300 305 Trp Ala Thr Gln Glu Arg Ile Ser Leu Gln Trp Leu Arg Arg Ile Gln 310 315 320 325 Asn Tyr Ser Val Met Asp Ile Cys Asp Tyr Asp Glu Ser Ser Gly Arg 330 335 340 Trp Asn Cys Leu Val Ala Arg Gln His Ile Glu Met Ser Thr Thr Gly 345 350 355 Trp Val Gly Arg Phe Arg Pro Ser Glu Pro His Phe Thr Leu Asp Gly 360 365 370 Asn Ser Phe Tyr Lys Ile Ile Ser Asn Glu Glu Gly Tyr Arg His Ile 375 380 385 Cys Tyr Phe Gln Ile Asp Lys Lys Asp Cys Thr Phe Ile Thr Lys Gly 390 395 400 405 Thr Trp Glu Val Ile Gly Ile Glu Ala Leu Thr Ser Asp Tyr Leu Tyr 410 415 420 Tyr Ile Ser Asn Glu Tyr Lys Gly Met Pro Gly Gly Arg Asn Leu Tyr 425 430 435 Lys Ile Gln Leu Ser Asp Tyr Thr Lys Val Thr Cys Leu Ser Cys Glu 440 445 450 Leu Asn Pro Glu Arg Cys Gln Tyr Tyr Ser Val Ser Phe Ser Lys Glu 455 460 460 Ala Lys Tyr Tyr Gln Leu Arg Cys Ser Gly Pro Gly Leu Pro Leu Tyr 465 470 475 480 Thr Leu His Ser Ser Val Asn Asp Lys Gly Leu Arg Val Leu Glu Asp 485 490 495 Asn Ser Ala Leu Asp Lys Met Leu Gln Asn Val Gln Met Pro Ser Lys 500 505 510 Lys Leu Asp Phe Ile Ile Leu Asn Glu Thr Lys Phe Trp Tyr Gln Met 515 520 525 Ile Leu Pro Pro His Phe Asp Lys Ser Lys Lys Tyr Pro Leu Leu Leu 530 535 540 Asp Val Tyr Ala Gly Pro Cys Ser Gln Lys Ala Asp Thr Val Phe Arg 545 550 555 560 Leu Asn Trp Ala Thr Tyr Leu Ala Ser Thr Glu Asn Ile Ile Val Ala 565 570 575 Ser Phe Asp Gly Arg Gly Ser Gly Tyr Gln Gly Asp Lys Ile Met His 580 585 590 Ala Ile Asn Arg Arg Leu Gly Thr Phe Glu Val Glu Asp Gln Ile Glu 595 600 605 Ala Ala Arg Gln Phe Ser Lys Met Gly Phe Val Asp Asn Lys Arg Ile 610 615 620 Ala Ile Trp Gly Trp Ser Tyr Gly Gly Tyr Val Thr Ser Met Val Leu 625 630 635 640 Gly Ser Gly Ser Gly Val Phe Lys Cys Gly Ile Ala Val Ala Pro Val 645 650 655 Ser Arg Trp Glu Tyr Tyr Asp Ser Val Tyr Thr Glu Arg Tyr Met Gly 660 665 670 Leu Pro Thr Pro Glu Asp Asn Leu Asp His Tyr Arg Asn Ser Thr Val 675 680 685 Met Ser Arg Ala Glu Asn Phe Lys Gln Val Glu Tyr Leu Leu Ile His 690 695 700 Gly Thr Ala Asp Asp Asn Val His Phe Gln Gln Ser Ala Gln Ile Ser 705 710 715 720 Lys Ala Leu Val Asp Val Gly Val Asp Phe Gln Ala Met Trp Tyr Thr 725 730 735 Asp Glu Asp His Gly Ile Ala Ser Ser Thr Ala His Gln His Ile Tyr 740 745 750 Thr His Met Ser His Phe Ile Lys Gln Cys Phe Ser Leu Pro 755 760 765 7 amino acids amino acid linear The first Xaa is either Trp or Phe. 4 Xaa Gly Trp Ser Tyr Gly Gly 5 7 amino acids amino acid linear 5 Phe Gly Lys Asp Tyr Gly Gly 5 7 amino acids amino acid linear Xaa is either Ala or Gly 6 Gly Thr Xaa Asp Asp Asn Val 5 7 amino acids amino acid linear 7 Ala Gln Asn His Gly Leu Ser 5 7 amino acids amino acid linear The first Xaa is Glu or Ser. When the first Xaa is Glu, the second Xaa is Gly and the third is Ala. When the first Xaa is Ser, the second Xaa is Ser, and the third Xaa is Arg. 8 Asp Xaa Asp His Xaa Ile Xaa 5 7 amino acids amino acid linear Xaa is Pro or Ala. 9 Xaa Thr Ala Asp Glu Lys Ile 5 7 amino acids amino acid linear Xaa is Thr, His or Ser. 10 Asp Glu Ser His Tyr Phe Xaa 5 

We claim:
 1. Isolated, dimeric FAPα molecule, having a molecular weight of about 170 kilodaltons as determined by SDS-PAGE, wherein said dimeric FAPα molecule is capable of degrading extracellular matrix proteins.
 2. The dimeric FAPα molecule of claim 1, wherein each monomer of said dimeric FAPα molecule consists of the amino acid sequence of SEQ ID NO:
 2. 3. The dimeric FAPα molecule of claim 1, produced recombinantly.
 4. The dimeric FAPα molecule of claim 3, produced by a eukaryotic cell.
 5. Isolated protein consisting of: (i) the FAPα catalytic domain, and (ii) at least one portion of a non FAPα protein.
 6. Method for cleaving a terminal dipeptide of formula Xaa-Pro from a molecule, comprising contacting said molecule with a second molecule, said second molecule having FAPα enzymatic activity.
 7. The method of claim 6, wherein said second molecule is isolated, dimeric FAPα.
 8. The method of claim 6, wherein said second molecule comprises an FAPα catalytic domain.
 9. Method for identifying an enzyme inhibitor, comprising combining: (i) a molecule having FAPα enzymatic activity; (ii) a substrate for said molecule; (iii) a substance believed to be an enzyme inhibitor; and (iv) determining activity of (i) on (ii), wherein a decrease in activity when (iii) is present as compared to activity when (iii) is absent indicates that said substance is an enzyme inhibitor.
 10. The method of claim 9, wherein said molecule is isolated dimeric FAPα.
 11. The method of claim 9, wherein said molecule comprises an FAPα catalytic domain.
 12. Method for treating a subject with a pathological condition characterized by FAPα expression, comprising administering to said subject an amount of a FAPα inhibitor sufficient to inhibit enzyme activity of FAPα.
 13. The method of claim 12, wherein said inhibitor is a monoclonal antibody.
 14. The method of claim 12, wherein said inhibitor is a collagen derivative.
 15. The method of claim 12, wherein said pathological condition is a cancer. 